Chemical shift difference analysis of the long Taspase1 loop.

<p>Analysis of the chemical shift differences with respect to random coil values for H_α, C_α, and C_β shifts of the Taspase1 loop. Helices according to the secondary structure prediction are depicted on top. Note that stretches of negative H_α and C_β values, as well as positive C_α values indicate a helical conformation of the respective amino acids.</p

Secondary structure predictions of Taspase1 loop.

<p>Primary sequence based secondary structure predictions of the loop region Gly178-Asp233 of Taspase1, which is missing in the crystal structure of active Taspase1 (PDB 2a8j). The algorithms predict a stretch of helices between Asn185 and Ser223. For the YASARA model and the JNet prediction, cylinders represent helical areas, lines represent random coil and loops are represented as curves. Confidence (conf) values range from 0 (uncertain) to 9 (confident). Residues predicted as buried by sol25 and sol0 are labeled (B).</p

Spectroscopic analysis and MD simulation of the Taspase1 loop at the C-terminus of the α-subunit.

<p>(a) CD spectra of the long (G178-D233; red) and the short Taspase1 loop (P183-S222; black) show a helical structure for both peptides. (b) CD spectrum based secondary structure deconvolution using CDSSTR confirms a higher helical content (green) in the long loop compared to the short loop. Numbers are given in percent. (c) Three 10 ns molecular dynamics simulations were performed in YASARA starting with a linear loop peptide. For each amino acid, the time of the respective amino acid in helix, sheet, turn or random coil conformation is plotted. (d) Representative snapshots of the simulations indicate the formation of helices, especially around Arg190.</p

Type 2 asparaginase loop models.

<p>Modeled structures of the Taspase1 loop homologous regions in other type 2 asparaginases generated with YASARA. The loop of human Taspase1 (template PDB 2a8i; 25 modeled amino acids) is predicted as predominantly helical, while for human glycosylasparaginase (template PDB 1apy; 20 modeled aa), human asparaginase (template PDB 4pvs; 14 modeled aa), plant asparaginase (template PDB 2gez; 33 modeled aa), <i>E</i>. <i>coli</i> asparaginase (template PDB 2zal; 17 modeled aa), and <i>F</i>. <i>meningosepticum</i> glycosylasparaginase (template PDB 1ayy; 10 modeled aa) mainly random coil elements are predicted. The modeled loop regions are highlighted in red; the active site (corresponding to Thr234 in Taspase1) is highlighted in green.</p

Additional file 1: Figure S1. of NmPin from the marine thaumarchaeote Nitrosopumilus maritimus is an active membrane associated prolyl isomerase

Sequence alignment of NmPin from N. maritimus with various homologues from other phyla to investigate a potential conservation of the positively charged lysine patch of NmPin. Representatives were found by BLAST search. Each group was separately aligned to NmPin (green). Lysines of the patch (K5, K7, K31, K34, K37, K47, K48, K90) are labelled in dark blue and Arg or positively charged residues which are in close proximity to the conserved position are labelled in light blue. The positively charged patch on the surface of NmPin might be conserved also in other members of the TACK phylum. (PDF 464 kb

Detection of polyomaviruses in gastrointestinal and lymphoid organs with generic PCR.

a<p>Detected with generic PCR.</p

Detection of HPyV12 with PCR.

a<p>Samples collected for BKPyV infection diagnosis.</p>b<p>From patients under natalizumab (Tysabri) therapy.</p>c<p>Samples collected for herpesvirus infection diagnosis.</p>d<p>Samples collected for JCPyV infection diagnosis.</p>e<p>Combined results of specific nested PCR and real-time PCR; samples were considered as positive if the result could be independently reproduced on different days.</p

Phylogenetic analysis of HPyV12.

<p>A Bayesian chronogram was deduced from the analysis of a 488 amino acid alignment of LTAg sequences. Polyomaviruses identified from human hosts are in red, from apes in blue. The human polyomaviruses MXPyV and the US strain of MWPyV have the same phylogenetic position as HPyV10 and are not shown. The sequence of the very recently discovered human STLPyV which is most closely related to HPyV10, MWPyV and MXPyV, became only available at the end of the revision process of this manuscript; it was therefore not included in the datasets put together for the present study. Statistical support for branches is given as posterior probability/bootstrap. For three branches defining potentially meaningful bipartitions (with respect to the question of the phylogenetic placement of HPyV12), statistical support observed for the corresponding bipartitions in the VP2 and VP1 analyses is also shown (grey panels). Hyphen indicates that bipartition was not observed in the ML or Bayesian tree. The scale axis is in amino acid substitution per site. This chronogram was rooted using a relaxed clock. A maximum likelihood analysis of the same dataset concluded to a similar topology and is thus not shown here.</p

Genome organization of HPyV12.

<p>Putative coding regions for VP1 to VP3, STAg antigen, and LTAg antigen are marked by arrows.</p

Reactivity of human sera to VP1 of HPyV12.

<p>The percentage of seroreactivity of pediatric sera (n = 74; 2–11 years) and sera of healthy adolescents and adults (n = 299; age: 16–72 years) in ELISA is shown. The results were stratified by age.</p